[BioC] problem with loading DESeq after upgrading from R 2.14 to R 2.15

[Yue Li]

Hi Steve,

Thanks for prompt reply! It's just that having to re-install all of the packages for every upgrade of R is also a hassle, don't u think? But you're right that installing it improperly is even disastrous like what I am experiencing now.

I wish in the future, someone could just make the upgrade of R as easy as upgrading iTunes or something like that.   

Yue


On 2012-04-23, at 3:53 PM, Steve Lianoglou wrote:

> Hi,
> 
> The way you are trying to maintain your libraries is generally frowned
> upon. You shouldn't be trying to use R-2.14 packages with your R-2.14
> install. You are exposing yourself to weird and hard to explain
> problems.
> 
> Look at the error message you are getting:
> 
> On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli at cs.toronto.edu> wrote:
> [snip]
>> Loading required package: locfit
>> locfit 1.5-7     2012-03-22
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so':
>> dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib
>> Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so
>> Reason: image not found
>> Error: package/namespace load failed for ‘DESeq’
> 
> Your trying to load a package from your 2.14 repo ... I'm not sure why
> this works from the terminal and not the GUI (are you sure you are
> firing up 2.15 from the terminal?), but I'm also not too inclined to
> smoke this out, because ... well, you shouldn't be doing this ;-) and
> also it will likely take you less time to just install things "the
> normal way".
> 
> If you really have some compelling reason to have a custom library
> structure, I like the way the bioc folks suggest developers to keep
> bioc-devel package separate from bioc-release (now that R is on an
> annual release cycle), eg:
> 
> http://www.bioconductor.org/developers/useDevel/
> 
> You could imagine having R-2.14 and R-2.15 in separate dirs instead of
> 2.15-release and 2.15-devel if working w/ devel libraries isn't your
> cup of tea -- but note they still keep different versions different.
> 
> Anyway, the "normal" R install does this for you anyway on OS X, so
> dollars-to-donuts you'll have less hassles just going "the normal"
> route, and installing the package you need via biocLite again in your
> "clean" 2.15 library path will likely cost less time than trying to
> debug your custom library path woes.
> 
> HTH,
> -steve
> 
> 
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
> | Memorial Sloan-Kettering Cancer Center
> | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact